Contacts of the strand formed by residues 450 - 454 (chain B) in PDB entry 3BJT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 450 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B ILE* 3.5 15.3 - - + +
430B VAL* 3.9 18.2 - - + -
438B ALA* 4.3 17.7 - - + +
441B VAL* 3.6 8.3 - - + -
442B ALA* 3.4 38.4 - - + +
446B PRO* 3.4 35.9 - - + -
448B ALA 3.9 1.3 - - - +
449B PRO* 1.3 68.9 - - - +
451B ILE* 1.3 63.0 + - - +
452B ALA 3.5 0.7 + - - -
467B ARG 4.5 1.8 - - - +
468B GLY* 2.9 23.3 + - - +
469B ILE* 3.3 7.8 - - + +
470B PHE* 2.8 26.4 + - - -
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Residues in contact with ILE 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B ALA* 3.9 15.0 - - + -
428B ILE 3.1 6.1 + - - +
429B ILE* 3.4 13.0 - - + +
430B VAL* 2.9 28.4 + - - +
449B PRO 3.4 2.2 + - - +
450B ILE* 1.3 72.8 - - - +
452B ALA* 1.3 60.1 + - - +
453B VAL* 3.9 1.9 + - + -
470B PHE* 3.5 15.3 - - + +
472B VAL* 4.1 21.5 - - + -
493B ALA* 4.2 22.2 - - + +
497B GLY* 4.6 6.7 - - - -
502B PHE* 4.0 30.3 - - + -
503B PHE* 3.9 30.3 - - + -
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Residues in contact with ALA 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B VAL 3.3 6.1 - - - +
432B THR* 4.5 8.1 - - + -
438B ALA* 3.9 20.2 - - + -
450B ILE* 3.5 1.6 + - + +
451B ILE* 1.3 71.7 - - - +
453B VAL* 1.3 62.4 + - - +
454B THR* 3.8 6.2 + - + +
463B ALA* 5.3 3.4 - - + -
469B ILE* 3.7 25.6 - - + -
470B PHE 2.9 10.9 + - - +
471B PRO* 3.8 2.7 - - + +
472B VAL 3.0 26.7 + - - +
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Residues in contact with VAL 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B ILE* 4.3 9.0 - - + -
430B VAL 2.9 9.5 + - - +
431B LEU* 3.6 10.7 - - + +
432B THR 3.3 22.4 + - - +
451B ILE* 4.5 2.2 - - + -
452B ALA* 1.3 74.5 - - - +
454B THR* 1.3 61.8 + - - +
472B VAL* 3.4 13.7 - - + +
474B CYS* 4.5 3.6 - - + -
489B ARG* 3.7 44.1 + - + +
492B PHE* 4.0 14.6 - - + -
493B ALA* 3.3 37.0 - - + +
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Residues in contact with THR 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B THR* 2.7 29.1 + - + -
433B LYS* 3.5 3.3 + - - -
452B ALA* 4.7 7.0 - - + +
453B VAL* 1.3 73.8 - - - +
455B ARG* 1.3 63.5 + - - +
456B ASN* 3.2 29.5 + - - +
459B THR* 3.4 18.9 + - - +
460B ALA* 4.1 18.2 - - + -
471B PRO* 6.3 0.4 - - + -
472B VAL 3.4 7.0 + - - +
473B LEU* 3.5 4.2 - - - -
474B CYS* 3.0 25.7 + - - -
489B ARG* 5.8 2.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il